The entire SWC Senate/Shadow War/Aflame stuff goes to great pains to mention that the Alliance and NGE are political parties in the Senate. Hell, it even mentioned, once, that the Triumvirate (the Legacy series government) is too busy with the real issues to pay attention to whatever is going on in the Unknown Regions, or in the Senate. I like to keep things vague so canon doesn't make me cry.

I even managed to squeeze a Sith Empire into the time period from 5.5 ABY to 6.5 ABY with one game, led by Lord Garonnin, a very minor character from Children of the Jedi.